1 ## plot.phylo.R (2011-03-23)
5 ## Copyright 2002-2011 Emmanuel Paradis
7 ## This file is part of the R-package `ape'.
8 ## See the file ../COPYING for licensing issues.
10 plot.phylo <- function(x, type = "phylogram", use.edge.length = TRUE,
11 node.pos = NULL, show.tip.label = TRUE,
12 show.node.label = FALSE, edge.color = "black",
13 edge.width = 1, edge.lty = 1, font = 3, cex = par("cex"),
14 adj = NULL, srt = 0, no.margin = FALSE,
15 root.edge = FALSE, label.offset = 0, underscore = FALSE,
16 x.lim = NULL, y.lim = NULL, direction = "rightwards",
17 lab4ut = "horizontal", tip.color = "black", ...)
19 Ntip <- length(x$tip.label)
21 warning("found only one tip in the tree")
24 if (any(tabulate(x$edge[, 1]) == 1))
25 stop("there are single (non-splitting) nodes in your tree; you may need to use collapse.singles()")
27 .nodeHeight <- function(Ntip, Nnode, edge, Nedge, yy)
28 .C("node_height", as.integer(Ntip), as.integer(Nnode),
29 as.integer(edge[, 1]), as.integer(edge[, 2]),
30 as.integer(Nedge), as.double(yy),
31 DUP = FALSE, PACKAGE = "ape")[[6]]
33 .nodeDepth <- function(Ntip, Nnode, edge, Nedge)
34 .C("node_depth", as.integer(Ntip), as.integer(Nnode),
35 as.integer(edge[, 1]), as.integer(edge[, 2]),
36 as.integer(Nedge), double(Ntip + Nnode),
37 DUP = FALSE, PACKAGE = "ape")[[6]]
39 .nodeDepthEdgelength <- function(Ntip, Nnode, edge, Nedge, edge.length)
40 .C("node_depth_edgelength", as.integer(Ntip),
41 as.integer(Nnode), as.integer(edge[, 1]),
42 as.integer(edge[, 2]), as.integer(Nedge),
43 as.double(edge.length), double(Ntip + Nnode),
44 DUP = FALSE, PACKAGE = "ape")[[7]]
46 Nedge <- dim(x$edge)[1]
49 type <- match.arg(type, c("phylogram", "cladogram", "fan",
50 "unrooted", "radial"))
51 direction <- match.arg(direction, c("rightwards", "leftwards",
52 "upwards", "downwards"))
53 if (is.null(x$edge.length)) use.edge.length <- FALSE
55 ## the order of the last two conditions is important:
56 if (type %in% c("unrooted", "radial") || !use.edge.length ||
57 is.null(x$root.edge) || !x$root.edge) root.edge <- FALSE
58 if (type == "fan" && root.edge) {
59 warning("drawing root edge with type = 'fan' is not yet supported")
63 phyloORclado <- type %in% c("phylogram", "cladogram")
64 horizontal <- direction %in% c("rightwards", "leftwards")
65 xe <- x$edge # to save
67 ## we first compute the y-coordinates of the tips.
68 phyOrder <- attr(x, "order")
69 ## make sure the tree is in cladewise order:
70 if (is.null(phyOrder) || phyOrder != "cladewise") {
71 x <- reorder(x) # fix from Klaus Schliep (2007-06-16)
72 if (!identical(x$edge, xe)) {
73 ## modified from Li-San Wang's fix (2007-01-23):
74 ereorder <- match(x$edge[, 2], xe[, 2])
75 if (length(edge.color) > 1) {
76 edge.color <- rep(edge.color, length.out = Nedge)
77 edge.color <- edge.color[ereorder]
79 if (length(edge.width) > 1) {
80 edge.width <- rep(edge.width, length.out = Nedge)
81 edge.width <- edge.width[ereorder]
83 if (length(edge.lty) > 1) {
84 edge.lty <- rep(edge.lty, length.out = Nedge)
85 edge.lty <- edge.lty[ereorder]
89 ### By contrats to ape (< 2.4), the arguments edge.color, etc., are
90 ### not elongated before being passed to segments(), except if needed
92 yy <- numeric(Ntip + Nnode)
93 TIPS <- x$edge[x$edge[, 2] <= Ntip, 2]
96 ## 'z' is the tree in pruningwise order used in calls to .C
97 z <- reorder(x, order = "pruningwise")
98 ### edge.color <- rep(edge.color, length.out = Nedge)
99 ### edge.width <- rep(edge.width, length.out = Nedge)
100 ### edge.lty <- rep(edge.lty, length.out = Nedge)
101 ### ## fix from Li-San Wang (2007-01-23):
103 ### x <- reorder(x, order = "pruningwise")
104 ### ereorder <- match(x$edge[, 2], xe[, 2])
105 ### edge.color <- edge.color[ereorder]
106 ### edge.width <- edge.width[ereorder]
107 ### edge.lty <- edge.lty[ereorder]
110 if (is.null(node.pos)) {
112 if (type == "cladogram" && !use.edge.length) node.pos <- 2
115 yy <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
117 ## node_height_clado requires the number of descendants
118 ## for each node, so we compute `xx' at the same time
119 ans <- .C("node_height_clado", as.integer(Ntip),
120 as.integer(Nnode), as.integer(z$edge[, 1]),
121 as.integer(z$edge[, 2]), as.integer(Nedge),
122 double(Ntip + Nnode), as.double(yy),
123 DUP = FALSE, PACKAGE = "ape")
127 if (!use.edge.length) {
128 if (node.pos != 2) xx <- .nodeDepth(Ntip, Nnode, z$edge, Nedge) - 1
131 xx <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
133 } else switch(type, "fan" = {
134 ## if the tips are not in the same order in tip.label
135 ## and in edge[, 2], we must reorder the angles: we
136 ## use `xx' to store temporarily the angles
137 TIPS <- x$edge[which(x$edge[, 2] <= Ntip), 2]
138 xx <- seq(0, 2*pi*(1 - 1/Ntip), 2*pi/Ntip)
139 theta <- double(Ntip)
141 theta <- c(theta, numeric(Nnode))
142 theta <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, theta)
143 if (use.edge.length) {
144 r <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
146 r <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
152 nb.sp <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
153 XY <- if (use.edge.length)
154 unrooted.xy(Ntip, Nnode, z$edge, z$edge.length, nb.sp)
156 unrooted.xy(Ntip, Nnode, z$edge, rep(1, Nedge), nb.sp)
157 ## rescale so that we have only positive values
158 xx <- XY$M[, 1] - min(XY$M[, 1])
159 yy <- XY$M[, 2] - min(XY$M[, 2])
161 X <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
165 ## angle (1st compute the angles for the tips):
166 yy <- c((1:Ntip)*2*pi/Ntip, rep(0, Nnode))
167 Y <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
175 xx <- tmp - min(tmp) + 1
178 if (direction == "rightwards") xx <- xx + x$root.edge
179 if (direction == "upwards") yy <- yy + x$root.edge
182 if (no.margin) par(mai = rep(0, 4))
183 if (is.null(x.lim)) {
187 pin1 <- par("pin")[1] # width of the device in inches
188 strWi <- strwidth(x$tip.label, "inches") # id. for the tip labels
189 ## 1.04 comes from that we are using a regular axis system
190 ## with 4% on both sides of the range of x:
191 xx.tips <- xx[1:Ntip] * 1.04
192 ## 'alp' is the conversion coefficient from
193 ## user coordinates to inches:
194 alp <- try(uniroot(function(a) max(a*xx.tips + strWi) - pin1,
195 c(0, 1e6))$root, silent = TRUE)
196 ## if the above fails, give 1/3 of the device for the tip labels:
197 if (is.character(alp)) tmp <- max(xx.tips)*1.5 else {
198 tmp <- if (show.tip.label) max(xx.tips + strWi/alp) else max(xx.tips)
201 } else x.lim <- c(1, Ntip)
202 } else switch(type, "fan" = {
203 if (show.tip.label) {
204 offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
205 x.lim <- c(min(xx) - offset, max(xx) + offset)
206 } else x.lim <- c(min(xx), max(xx))
208 if (show.tip.label) {
209 offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
210 x.lim <- c(0 - offset, max(xx) + offset)
211 } else x.lim <- c(0, max(xx))
213 if (show.tip.label) {
214 offset <- max(nchar(x$tip.label) * 0.03 * cex)
215 x.lim <- c(-1 - offset, 1 + offset)
216 } else x.lim <- c(-1, 1)
218 } else if (length(x.lim) == 1) {
220 if (phyloORclado && !horizontal) x.lim[1] <- 1
221 if (type %in% c("fan", "unrooted") && show.tip.label)
222 x.lim[1] <- -max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
223 if (type == "radial")
225 if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.03 * cex)
229 if (phyloORclado && direction == "leftwards") xx <- x.lim[2] - xx
230 if (is.null(y.lim)) {
232 if (horizontal) y.lim <- c(1, Ntip) else {
234 pin2 <- par("pin")[2] # height of the device in inches
235 strWi <- strwidth(x$tip.label, "inches")
236 ## 1.04 comes from that we are using a regular axis system
237 ## with 4% on both sides of the range of x:
238 yy.tips <- yy[1:Ntip] * 1.04
239 ## 'alp' is the conversion coefficient from
240 ## user coordinates to inches:
241 alp <- try(uniroot(function(a) max(a*yy.tips + strWi) - pin2,
242 c(0, 1e6))$root, silent = TRUE)
243 ## if the above fails, give 1/3 of the device for the tip labels:
244 if (is.character(alp)) tmp <- max(yy.tips)*1.5 else {
245 tmp <- if (show.tip.label) max(yy.tips + strWi/alp) else max(yy.tips)
249 } else switch(type, "fan" = {
250 if (show.tip.label) {
251 offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
252 y.lim <- c(min(yy) - offset, max(yy) + offset)
253 } else y.lim <- c(min(yy), max(yy))
255 if (show.tip.label) {
256 offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
257 y.lim <- c(0 - offset, max(yy) + offset)
258 } else y.lim <- c(0, max(yy))
260 if (show.tip.label) {
261 offset <- max(nchar(x$tip.label) * 0.03 * cex)
262 y.lim <- c(-1 - offset, 1 + offset)
263 } else y.lim <- c(-1, 1)
265 } else if (length(y.lim) == 1) {
267 if (phyloORclado && horizontal) y.lim[1] <- 1
268 if (type %in% c("fan", "unrooted") && show.tip.label)
269 y.lim[1] <- -max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
270 if (type == "radial")
271 y.lim[1] <- if (show.tip.label) -1 - max(nchar(x$tip.label) * 0.018 * max(yy) * cex) else -1
274 if (phyloORclado && direction == "downwards") yy <- y.lim[2] - yy
275 if (phyloORclado && root.edge) {
276 if (direction == "leftwards") x.lim[2] <- x.lim[2] + x$root.edge
277 if (direction == "downwards") y.lim[2] <- y.lim[2] + x$root.edge
279 asp <- if (type %in% c("fan", "radial", "unrooted")) 1 else NA # fixes by Klaus Schliep (2008-03-28 and 2010-08-12)
280 plot(0, type = "n", xlim = x.lim, ylim = y.lim, ann = FALSE, axes = FALSE, asp = asp, ...)
282 adj <- if (phyloORclado && direction == "leftwards") 1 else 0
283 if (phyloORclado && show.tip.label) {
284 MAXSTRING <- max(strwidth(x$tip.label, cex = cex))
286 if (direction == "rightwards") {
287 lox <- label.offset + MAXSTRING * 1.05 * adj
289 if (direction == "leftwards") {
290 lox <- -label.offset - MAXSTRING * 1.05 * (1 - adj)
291 #xx <- xx + MAXSTRING
295 MAXSTRING <- MAXSTRING * 1.09 * (psr[4] - psr[3])/(psr[2] - psr[1])
296 loy <- label.offset + MAXSTRING * 1.05 * adj
299 if (direction == "downwards") {
301 ##yy <- yy + MAXSTRING
306 if (type == "phylogram") {
307 phylogram.plot(x$edge, Ntip, Nnode, xx, yy,
308 horizontal, edge.color, edge.width, edge.lty)
311 ereorder <- match(z$edge[, 2], x$edge[, 2])
312 if (length(edge.color) > 1) {
313 edge.color <- rep(edge.color, length.out = Nedge)
314 edge.color <- edge.color[ereorder]
316 if (length(edge.width) > 1) {
317 edge.width <- rep(edge.width, length.out = Nedge)
318 edge.width <- edge.width[ereorder]
320 if (length(edge.lty) > 1) {
321 edge.lty <- rep(edge.lty, length.out = Nedge)
322 edge.lty <- edge.lty[ereorder]
324 circular.plot(z$edge, Ntip, Nnode, xx, yy, theta,
325 r, edge.color, edge.width, edge.lty)
327 cladogram.plot(x$edge, xx, yy, edge.color, edge.width, edge.lty)
331 "rightwards" = segments(0, yy[ROOT], x$root.edge, yy[ROOT]),
332 "leftwards" = segments(xx[ROOT], yy[ROOT], xx[ROOT] + x$root.edge, yy[ROOT]),
333 "upwards" = segments(xx[ROOT], 0, xx[ROOT], x$root.edge),
334 "downwards" = segments(xx[ROOT], yy[ROOT], xx[ROOT], yy[ROOT] + x$root.edge))
335 if (show.tip.label) {
336 if (is.expression(x$tip.label)) underscore <- TRUE
337 if (!underscore) x$tip.label <- gsub("_", " ", x$tip.label)
340 text(xx[1:Ntip] + lox, yy[1:Ntip] + loy, x$tip.label, adj = adj,
341 font = font, srt = srt, cex = cex, col = tip.color)
343 if (type == "unrooted") {
344 if (lab4ut == "horizontal") {
345 y.adj <- x.adj <- numeric(Ntip)
346 sel <- abs(XY$axe) > 0.75 * pi
347 x.adj[sel] <- -strwidth(x$tip.label)[sel] * 1.05
348 sel <- abs(XY$axe) > pi/4 & abs(XY$axe) < 0.75 * pi
349 x.adj[sel] <- -strwidth(x$tip.label)[sel] * (2 * abs(XY$axe)[sel] / pi - 0.5)
350 sel <- XY$axe > pi / 4 & XY$axe < 0.75 * pi
351 y.adj[sel] <- strheight(x$tip.label)[sel] / 2
352 sel <- XY$axe < -pi / 4 & XY$axe > -0.75 * pi
353 y.adj[sel] <- -strheight(x$tip.label)[sel] * 0.75
354 text(xx[1:Ntip] + x.adj * cex, yy[1:Ntip] + y.adj * cex,
355 x$tip.label, adj = c(adj, 0), font = font,
356 srt = srt, cex = cex, col = tip.color)
357 } else { # if lab4ut == "axial"
358 adj <- abs(XY$axe) > pi/2
359 srt <- 180 * XY$axe / pi
360 srt[adj] <- srt[adj] - 180
361 adj <- as.numeric(adj)
362 xx.tips <- xx[1:Ntip]
363 yy.tips <- yy[1:Ntip]
365 xx.tips <- xx.tips + label.offset * cos(XY$axe)
366 yy.tips <- yy.tips + label.offset * sin(XY$axe)
368 ## `srt' takes only a single value, so can't vectorize this:
369 ## (and need to 'elongate' these vectors:)
370 font <- rep(font, length.out = Ntip)
371 tip.color <- rep(tip.color, length.out = Ntip)
372 cex <- rep(cex, length.out = Ntip)
374 text(xx.tips[i], yy.tips[i], cex = cex[i],
375 x$tip.label[i], adj = adj[i], font = font[i],
376 srt = srt[i], col = tip.color[i])
379 if (type %in% c("fan", "radial")) {
380 xx.tips <- xx[1:Ntip]
381 yy.tips <- yy[1:Ntip]
382 ## using atan2 considerably facilitates things compared to acos...
383 angle <- atan2(yy.tips, xx.tips) # in radians
385 xx.tips <- xx.tips + label.offset * cos(angle)
386 yy.tips <- yy.tips + label.offset * sin(angle)
389 angle <- angle * 180/pi # switch to degrees
390 angle[s] <- angle[s] + 180
392 ## `srt' takes only a single value, so can't vectorize this:
393 ## (and need to 'elongate' these vectors:)
394 font <- rep(font, length.out = Ntip)
395 tip.color <- rep(tip.color, length.out = Ntip)
396 cex <- rep(cex, length.out = Ntip)
398 text(xx.tips[i], yy.tips[i], x$tip.label[i], font = font[i],
399 cex = cex[i], srt = angle[i], adj = adj[i],
404 text(xx[ROOT:length(xx)] + label.offset, yy[ROOT:length(yy)],
405 x$node.label, adj = adj, font = font, srt = srt, cex = cex)
406 L <- list(type = type, use.edge.length = use.edge.length,
407 node.pos = node.pos, show.tip.label = show.tip.label,
408 show.node.label = show.node.label, font = font,
409 cex = cex, adj = adj, srt = srt, no.margin = no.margin,
410 label.offset = label.offset, x.lim = x.lim, y.lim = y.lim,
411 direction = direction, tip.color = tip.color,
412 Ntip = Ntip, Nnode = Nnode)
413 assign("last_plot.phylo", c(L, list(edge = xe, xx = xx, yy = yy)),
414 envir = .PlotPhyloEnv)
418 phylogram.plot <- function(edge, Ntip, Nnode, xx, yy, horizontal,
419 edge.color, edge.width, edge.lty)
421 nodes <- (Ntip + 1):(Ntip + Nnode)
427 ## un trait vertical à chaque noeud...
429 y0v <- y1v <- numeric(Nnode)
430 ## store the index of each node in the 1st column of edge:
431 NodeInEdge1 <- vector("list", Nnode)
434 j <- NodeInEdge1[[ii]] <- which(edge[, 1] == i)
435 tmp <- range(yy[edge[j, 2]])
439 ## ... et un trait horizontal partant de chaque tip et chaque noeud
445 nc <- length(edge.color)
446 nw <- length(edge.width)
447 nl <- length(edge.lty)
449 if (nc + nw + nl == 3) {
450 color.v <- edge.color
451 width.v <- edge.width
454 Nedge <- dim(edge)[1]
455 edge.color <- rep(edge.color, length.out = Nedge)
456 edge.width <- rep(edge.width, length.out = Nedge)
457 edge.lty <- rep(edge.lty, length.out = Nedge)
458 DF <- data.frame(edge.color, edge.width, edge.lty, stringsAsFactors = FALSE)
459 color.v <- rep("black", Nnode)
460 width.v <- rep(1, Nnode)
461 lty.v <- rep(1, Nnode)
463 br <- NodeInEdge1[[i]]
464 if (length(br) > 2) {
465 x <- unique(DF[br, 1])
466 if (length(x) == 1) color.v[i] <- x
467 x <- unique(DF[br, 2])
468 if (length(x) == 1) width.v[i] <- x
469 x <- unique(DF[br, 3])
470 if (length(x) == 1) lty.v[i] <- x
474 if (any(DF[A, ] != DF[B, ])) {
475 color.v[i] <- edge.color[B]
476 width.v[i] <- edge.width[B]
477 lty.v[i] <- edge.lty[B]
479 y0v <- c(y0v, y0v[i])
480 y1v <- c(y1v, yy[i + Ntip])
481 x0v <- c(x0v, x0v[i])
482 color.v <- c(color.v, edge.color[A])
483 width.v <- c(width.v, edge.width[A])
484 lty.v <- c(lty.v, edge.lty[A])
486 y0v[i] <- yy[i + Ntip]
488 color.v[i] <- edge.color[A]
489 width.v[i] <- edge.width[A]
490 lty.v[i] <- edge.lty[A]
497 segments(x0h, y0h, x1h, y0h, col = edge.color, lwd = edge.width, lty = edge.lty) # draws horizontal lines
498 segments(x0v, y0v, x0v, y1v, col = color.v, lwd = width.v, lty = lty.v) # draws vertical lines
500 segments(y0h, x0h, y0h, x1h, col = edge.color, lwd = edge.width, lty = edge.lty) # draws vertical lines
501 segments(y0v, x0v, y1v, x0v, col = color.v, lwd = width.v, lty = lty.v) # draws horizontal lines
505 cladogram.plot <- function(edge, xx, yy, edge.color, edge.width, edge.lty)
506 segments(xx[edge[, 1]], yy[edge[, 1]], xx[edge[, 2]], yy[edge[, 2]],
507 col = edge.color, lwd = edge.width, lty = edge.lty)
509 circular.plot <- function(edge, Ntip, Nnode, xx, yy, theta,
510 r, edge.color, edge.width, edge.lty)
511 ### 'edge' must be in pruningwise order
515 theta0 <- theta[edge[, 2]]
516 costheta0 <- cos(theta0)
517 sintheta0 <- sin(theta0)
524 segments(x0, y0, x1, y1, col = edge.color, lwd = edge.width, lty = edge.lty)
526 tmp <- which(diff(edge[, 1]) != 0)
527 start <- c(1, tmp + 1)
528 Nedge <- dim(edge)[1]
531 ## function dispatching the features to the arcs
532 foo <- function(edge.feat, default) {
533 if (length(edge.feat) == 1) return(rep(edge.feat, Nnode))
535 edge.feat <- rep(edge.feat, length.out = Nedge)
536 feat.arc <- rep(default, Nnode)
538 tmp <- edge.feat[start[k]]
539 if (tmp == edge.feat[end[k]]) feat.arc[k] <- tmp
544 co <- foo(edge.color, "black")
545 lw <- foo(edge.width, 1)
546 ly <- foo(edge.lty, 1)
551 X <- rep(r[edge[i, 1]], 100)
552 Y <- seq(theta[edge[i, 2]], theta[edge[j, 2]], length.out = 100)
553 lines(X*cos(Y), X*sin(Y), col = co[k], lwd = lw[k], lty = ly[k])
557 unrooted.xy <- function(Ntip, Nnode, edge, edge.length, nb.sp)
559 foo <- function(node, ANGLE, AXIS) {
560 ind <- which(edge[, 1] == node)
562 start <- AXIS - ANGLE/2
563 for (i in 1:length(sons)) {
564 h <- edge.length[ind[i]]
565 angle[sons[i]] <<- alpha <- ANGLE*nb.sp[sons[i]]/nb.sp[node]
566 axis[sons[i]] <<- beta <- start + alpha/2
567 start <- start + alpha
568 xx[sons[i]] <<- h*cos(beta) + xx[node]
569 yy[sons[i]] <<- h*sin(beta) + yy[node]
572 if (i > Ntip) foo(i, angle[i], axis[i])
574 Nedge <- dim(edge)[1]
575 yy <- xx <- numeric(Ntip + Nnode)
576 ## `angle': the angle allocated to each node wrt their nb of tips
577 ## `axis': the axis of each branch
578 axis <- angle <- numeric(Ntip + Nnode)
579 ## start with the root...
580 foo(Ntip + 1L, 2*pi, 0)
583 axe <- axis[1:Ntip] # the axis of the terminal branches (for export)
585 ## insures that returned angles are in [-PI, +PI]:
586 axe[axeGTpi] <- axe[axeGTpi] - 2*pi
587 list(M = M, axe = axe)
590 node.depth <- function(phy)
592 n <- length(phy$tip.label)
594 N <- dim(phy$edge)[1]
595 phy <- reorder(phy, order = "pruningwise")
596 .C("node_depth", as.integer(n), as.integer(m),
597 as.integer(phy$edge[, 1]), as.integer(phy$edge[, 2]),
598 as.integer(N), double(n + m), DUP = FALSE, PACKAGE = "ape")[[6]]
601 plot.multiPhylo <- function(x, layout = 1, ...)
604 layout(matrix(1:layout, ceiling(sqrt(layout)), byrow = TRUE))
605 else layout(matrix(1))
608 on.exit(par(ask = FALSE))
610 for (i in 1:length(x)) plot(x[[i]], ...)
613 trex <- function(phy, title = TRUE, subbg = "lightyellow3",
614 return.tree = FALSE, ...)
616 lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
617 devmain <- dev.cur() # where the main tree is plotted
619 restore <- function() {
621 assign("last_plot.phylo", lastPP, envir = .PlotPhyloEnv)
626 cat("Click close to a node. Right-click to exit.\n")
628 x <- identify.phylo(phy, quiet = TRUE)
629 if (is.null(x)) return(invisible(NULL)) else {
631 if (is.null(x)) cat("Try again!\n") else {
637 } else dev.set(devsub)
639 tr <- extract.clade(phy, x)
641 if (is.character(title)) title(title)
644 if (is.null(phy$node.label))
645 paste("From node #", x, sep = "")
646 else paste("From", phy$node.label[x - Ntip(phy)])
649 if (return.tree) return(tr)
656 kronoviz <- function(x, layout = length(x), horiz = TRUE, ...)
658 par(mar = rep(0.5, 4), oma = rep(2, 4))
659 rts <- sapply(x, function(x) branching.times(x)[1])
661 lim <- cbind(rts - maxrts, rts)
663 Ntips <- sapply(x, Ntip)
673 layout(matrix(1:layout, nrow), widths = w, heights = h)
674 if (layout > Ntree && !par("ask")) {
676 on.exit(par(ask = FALSE))
680 plot(x[[i]], x.lim = lim[i, ], ...)
683 plot(x[[i]], y.lim = lim[i, ], direction = "u", ...)
685 axisPhylo(if (horiz) 1 else 4) # better if the deepest tree is last ;)